Yamamoto et al. Human Genome Variation (2020) 7:8 https://doi.org/10.1038/s41439-020-0095-1 Human Genome Variation DATA REPORT Open Access Phenotypes of a family with XLH with a novel PHEX mutation Akiko Yamamoto 1, Toshiro Nakamura1,YasuhisaOhata 2, Takuo Kubota2 and Keiichi Ozono2 Abstract X-linked hypophosphatemia (XLH) is the most common form of heritable hypophosphatemic rickets. We encountered a 4-year-old boy with a novel variant in the phosphate-regulating neutral endopeptidase homolog X-linked (PHEX) gene who presented with a short stature, genu valgum, and scaphocephaly. The same mutation was identified in his mother and sister; however, the patient presented with a more severe case. X-linked hypophosphatemia (XLH) is an X-linked whereas his elder and younger brothers did not have a dominant disorder and the most common form of heri- short stature (Fig. 1(a)). table rickets, with a case rate estimate of ~1 case per At the time of his visit, his height was 95.4 cm 20,000 live births1. Inactive mutations in PHEX, which is (−2.51 standard deviation score (SDS)), weight was located in Xp22.1-22.2, have been implicated in the 14.8 kg (−1.13 SDS), and growth rate was 5.2 cm per year pathogenesis of XLH. More than 200 different mutations (−1.40 SDS), and genu valgum and scaphocephaly were in PHEX have been identified to date2. XLH is char- both evident. He did not have any dental issues or other acterized by rickets accompanied by bone deformities, a symptoms. fi 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; short stature, dental anomalies, bone pain, hearing dif - His serum calcium level was 9.71 mg/dl (normal culties, enthesopathy, and muscular dysfunction3. Patients range: 8.8–10.3 mg/dl), phosphate level was 2.4 mg/dl with XLH have hypophosphatemia with low levels of renal (3.8–5.9 mg/dl), alkaline phosphatase (ALP) level was phosphate reabsorption, normal serum calcium levels, 1175 IU/L (420–1200 mg/dl), intact parathyroid hor- elevated serum alkaline phosphatase activities, normal or mone (PTH) (ECLIA) level was 73 pg/ml (10–65 pg/ml), increased parathyroid hormone levels, normal or and 25(OH) vitamin D (RIA) level was 17 ng/ml increased 1,25-dihydroxyvitamin D3 levels, and elevated (>30 ng/ml). He had a low % tubular reabsorption of FGF23 levels4. Marked variations in XLH phenotypes phosphorus (TRP) value (89.3%) and a high intact FGF23 have been reported. We herein describe a boy and his (ELISA) level (73 pg/ml) (16–69 pg/ml). Bilateral femoral family who had XLH and a novel splice-site mutation in and tibial bowing with fraying and cupping of the meta- PHEX. physis were noted on the X-ray images (Fig. 1b). Brain CT A boy aged 4 years and 11 months presented with a scans showed craniosynostosis (Fig. 1c) and a mild Chiari short stature to the endocrinology unit of our hospital. He malformation. was born after a normal pregnancy, with a birth weight of Since XLH was suspected, a genetic analysis was per- 3130 g and body length of 48 cm. He had an elder brother formed, which was approved by the Institutional Review as well as a younger brother and sister. His mother and Boards of the participating institutions. Written informed grandmother both had a short stature and genu valgum, consent was obtained from the study participants, including their consent to participate and permission to publish the findings obtained. Genomic DNA was extracted from whole blood samples using a magLEAD Correspondence: Akiko Yamamoto ([email protected]) Consumable Kit (Precision System Science Co., Ltd., 1Department of Pediatrics, Kumamoto Chuo Hospital, Kumamoto, Japan 2Department of Pediatrics, Osaka University Graduate School of Medicine, Chiba, Japan). The amplicons generated by PCR with the Osaka, Japan © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a linktotheCreativeCommons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Official journal of the Japan Society of Human Genetics Yamamoto et al. Human Genome Variation (2020) 7:8 Page 2 of 3 Fig. 1 Clinical characteristics and genetic findings in the patient. a A family tree: the solid square indicates the index case. Solid circles indicate family members who developed rickets. Open symbols indicate healthy members. b A radiological examination showing fraying and cupping of the metaphysis and bilateral leg deformation. c Three-dimensional CT showing skull bone window reconstruction. The complete closure of sagittal sutures. d Gene analysis. A novel splice acceptor site mutation, c.1769-2delA, was identified in PHEX. The same heterozygous mutation was detected in the mother and sister of the patient. No mutations were found in the father. designed primers were Sanger sequenced using a 3730 common form of heritable rickets, and inactive mutations DNA analyzer (Applied Biosystems, Foster City, CA, in PHEX have been implicated in the pathogenesis of USA), which revealed a novel PHEX mutation in intron XLH. In accordance with the present results, splice-site 17, NM_000444.6: c.1769-2delA. We analyzed this novel mutations have been shown to be responsible for 17% of mutation by Human Splicing Finder 3.1 (http://www.umd. all reported PHEX mutations5. Other mutations have also be/HSF3/index.html), and the results obtained suggested been reported in the splice acceptor site of intron 172,6,7. that this mutation led to a broken WT acceptor site and Hue Yue et al. described a case of a 16-year-old boy with a affected splicing. The mutation detected in this patient PHEX gene mutation in the splice acceptor site of intron was not found in the Human Gene Mutation Database 17 (c.1768 + 2 T > G). This was a sporadic case that was (http://www.hgmd.cf.ac.uk/ac/index.php) or Genome characterized by leg bowing, hip pain, and growth retar- Aggregation Database (http://gnomad.broadinstitute.org). dation. In contrast, the present case had a familial The diagnosis of XLH was confirmed by a genetic analysis, mutation in PHEX along with a short stature, genu val- and therapy comprising phosphate 55 mg/kg/day and alfa- gum, and scaphocephaly. Scaphocephaly is a form of calcidol 35 ng/kg/day was initiated. DNA samples obtained craniosynostosis, a cranial malformation caused by pre- from the patient’s younger sister, mother, and father were mature fusing of the sagittal suture, and may develop in also subjected to a genetic analysis. No abnormalities were infants as young as 1 year of age3,8. Craniosynostosis detected in PHEX in the father, whereas the mother and occurs in ~60% of children with XLH9. Between 25% and sister had the same mutation. His mother and sister both 50% of children with XLH also have a Chiari type 1 had hypophosphatemia, elevated ALP enzyme activities, and malformation, which causes the cerebellar tonsils to high intact FGF23 levels (Table 1,Fig.1d). His mother also herniate through the foramen magnum9,10. The sister, had a short stature (148 cm) and genu valgum, whereas his mother, and grandmother of the patient in the present sister only presented with mild genu valgum (her height was report did not have scaphocephaly. In a large case series, −1.78 SD). Although we were unable to genetically analyze gender differences in the disease severity of XLH were not the DNA from his grandmother, she also had a short sta- observed7,11; however, the severity and clinical manifes- ture, genu valgum, and bone pain. tations of XLH patients varied markedly within the same We herein described a novel variant mutation in the family12. Among the family members tested, only the boy splice site of intron 17 in PHEX of a boy and his family presented with sagittal synostosis and a mild Chiari with XLH. XLH is a dominant disorder and the most malformation. Congenital forms of craniosynostosis Official journal of the Japan Society of Human Genetics Yamamoto et al. Human Genome Variation (2020) 7:8 Page 3 of 3 mostly develop in infancy, whereas those caused by metabolic disorders are more common in infants aged ~2 10 %TRP (%) years . Therefore, the younger sister was followed up for symptoms of craniosynostosis. In summary, we herein described the novel splicing of and a familial mutation in PHEX. An early diagnosis facilitates the rapid initiation of proper treatment. Since 25(OH) vitamin D (ng/ml) we detected the same mutation in the younger sister of the patient in our report, she underwent regular follow- ups. We will also carefully monitor symptoms and disease 2 progression in this family in the future. HGV database 1,25(OH) vitamin D (pg/ ml) The relevant data from this Data Report are hosted at the Human Genome Variation Database at https://doi.org/10.6084/m9.figshare.hgv.2823. Acknowledgements We thank the family for allowing us to report this case. intact FGF23 (pg/ml) Conflict of interest The authors declare that they have no conflict of interest.